Over recent decades, advancements in omics technologies, such as proteomics, genomics, epigenomics, metabolomics, transcriptomics, and microbiomics, have significantly enhanced our understanding of the molecular mechanisms underlying various physiological and pathological processes. Nonetheless, the analysis and interpretation of vast omics data concerning reproductive diseases are complicated by the cyclic regulation of hormones and multiple other factors, which, in conjunction with a genetic makeup of an individual, lead to diverse biological responses. Reproductomics investigates the interplay between a hormonal regulation of an individual, environmental factors, genetic predisposition (DNA composition and epigenome), health effects, and resulting biological outcomes. It is a rapidly emerging field that utilizes computational tools to analyze and interpret reproductive data, with the aim of improving reproductive health outcomes. It is time to explore the applications of reproductomics in understanding the molecular mechanisms underlying infertility, identification of potential biomarkers for diagnosis and treatment, and in improving assisted reproductive technologies (ARTs). Reproductomics tools include machine learning algorithms for predicting fertility outcomes, gene editing technologies for correcting genetic abnormalities, and single cell sequencing techniques for analyzing gene expression patterns at the individual cell level. However, there are several challenges, limitations and ethical issues involved with the use of reproductomics, such as the applications of gene editing technologies and their potential impact on future generations are discussed. The review comprehensively covers the applications and advancements of reproductomics, highlighting its potential to improve reproductive health outcomes and deepen our understanding of reproductive molecular mechanisms.
- MeSH
- Reproductive Techniques, Assisted trends MeSH
- Genomics MeSH
- Infertility genetics therapy diagnosis MeSH
- Humans MeSH
- Reproduction genetics physiology MeSH
- Machine Learning MeSH
- Computational Biology * MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Review MeSH
Bovine genes TLR4 and TLR5, which encode antibacterial toll-like receptors, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle to identify variants associated with reproduction, udder health, and milk production traits. Variants were discovered by hybrid resequencing of 164 bulls using HiSeq X-Ten and PacBio technologies and then individually genotyped. Nominal p-values < 0.05 for associations were detected in 18 combinations between 14 polymorphisms and 15 traits using one-way analysis of variance (ANOVA). The TLR4 variants g.610C>T (rs43578094) and g.10310T>G (rs8193072) in reference AC000135.1 were strictly associated with the index of early reproductive disorders and maternal calving ease, respectively, at false discovery rate (FDR) < 0.05. A highly permissive false discovery rate cutoff of 0.6 separated seventeen combinations in both genes comprising eight positives. In the case of the TLR4 variant g.9422T>C (rs8193060), indications were obtained for the association with as many as four reproductive traits: incidence of cystic ovaries, early reproductive disorders, calving ease, and production longevity. The permissive FDR interpretation for the TLR5 data indicated associations with cyst incidence and early reproduction disorders with maternal calving ease. Moreover, three TLR5 polymorphisms correlated with milk production traits. The discrepancy of the observed associations with the predicted impacts of the SNPs on protein function points to the role of haplotypes. Nevertheless, this question should be resolved on a larger scale. The observed associations are endorsed by independent evidence from the published functional roles in other species and by the published QTL mapping data.
- MeSH
- Polymorphism, Single Nucleotide MeSH
- Milk MeSH
- Immunity, Innate MeSH
- Reproduction genetics MeSH
- Cattle genetics MeSH
- Toll-Like Receptor 4 * genetics MeSH
- Toll-Like Receptor 5 * genetics MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Cattle genetics MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic MeSH
Recent advancements in the understanding of how sperm develop into offspring have shown complex interactions between environmental influences and genetic factors. The past decade, marked by a research surge, has not only highlighted the profound impact of paternal contributions on fertility and reproductive outcomes but also revolutionized our comprehension by unveiling how parental factors sculpt traits in successive generations through mechanisms that extend beyond traditional inheritance patterns. Studies have shown that offspring are more susceptible to environmental factors, especially during critical phases of growth. While these factors are broadly detrimental to health, their effects are especially acute during these periods. Moving beyond the immutable nature of the genome, the epigenetic profile of cells emerges as a dynamic architecture. This flexibility renders it susceptible to environmental disruptions. The primary objective of this review is to shed light on the diverse processes through which environmental agents affect male reproductive capacity. Additionally, it explores the consequences of paternal environmental interactions, demonstrating how interactions can reverberate in the offspring. It encompasses direct genetic changes as well as a broad spectrum of epigenetic adaptations. By consolidating current empirically supported research, it offers an exhaustive perspective on the interwoven trajectories of the environment, genetics, and epigenetics in the elaborate transition from sperm to offspring.
- MeSH
- Epigenesis, Genetic MeSH
- Phenotype MeSH
- Humans MeSH
- Disease Susceptibility MeSH
- Reproduction genetics MeSH
- Semen * MeSH
- Spermatozoa * MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Publication type
- Journal Article MeSH
- Review MeSH
The bovine genes TLR1, TLR2 and TLR6, which encode Toll-like receptors, key components of the innate immune system, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle, and the different variants present in the population were tested for association with reproductive and fitness traits. Diversity was investigated in a group of 164 bulls using hybrid resequencing of pooled amplicons with PacBio technology and of pooled genomic DNA using HiSeq X-Ten technology. The validated single nucleotide polymorphisms (SNPs) were genotyped in individual animals using the primer extension technique. The association of genotypic classes of 16 polymorphisms with six phenotypic traits were estimated with one-way analysis of variance (ANOVA) and with restricted maximum likelihood (REML) algorithm. The evaluated traits included the incidence of cystic ovaries, index of early reproductive disorders, paternal and maternal indicators of calving ease, production longevity and calf vitality index. The estimated breeding values were used for combined trait quantification. Early traits, namely, cystic ovaries and early reproductive disorders, were not associated with any of the tested polymorphisms according to the general ANOVA test. By contrast, five variants of all three genes were associated with calving ease, both paternal and maternal. The production longevity correlated with two variants of TLR1 and the calf vitality index correlated with the 1044 T > C (rs68268249) polymorphism in TLR2. The false discovery rate (FDR) according to Benjamini-Hochberg was favourable for the calving ease trait (0.221) and maternal calving ease (0.214), which allows to consider the observed associations real, regardless of the error arising from the multiple comparisons. These results were supported by REML only partially, probably in view of the additivity assumption. Two mechanisms of action on calving are conceivable, either via infection resistance or via the involvement of TLR2 in signalling in the myometrium. The known formation of heterodimers by the TLR1, -2 and -6 products might be responsible for the shared pattern of action in these genes. The association of the calf vitality index with TLR2 variation might reflect the increased role of infections in calves compared to adult animals.
- MeSH
- Breeding MeSH
- Longevity genetics MeSH
- Phenotype MeSH
- Genotype MeSH
- Polymorphism, Single Nucleotide * MeSH
- Reproduction genetics MeSH
- Cattle genetics MeSH
- Toll-Like Receptor 1 genetics MeSH
- Toll-Like Receptor 2 genetics MeSH
- Toll-Like Receptor 6 genetics MeSH
- Toll-Like Receptors genetics MeSH
- Age Factors MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Cattle genetics MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic MeSH
Optimization of chances for healthy offspring is thought to be one of the factors driving mate choice and compatibility of the major histocompatibility complex (MHC) is assumed to determine the offspring's fitness. While humans have been claimed to be able to perceive information of MHC compatibility via the olfactory channel, it remains unknown whether humans use such information for mate choice. By investigation of 3691 married couples, we observed that the high polymorphism of MHC leads to a low chance for homozygous offspring. MHC similarity between couples did not differ from chance, we hence observed no MHC effect in married couples. Hormonal contraception at the time of relationship initiation had no significant effect towards enhanced similarity. A low variety of alleles within a postcode area led to a higher likelihood of homozygous offspring. Based on this data, we conclude that there is no pattern of MHC dis-assortative mating in a genetically diverse Western society. We discuss the question of olfactory mate preference, in-group mating bias and the high polymorphism as potential explanations.
- MeSH
- Major Histocompatibility Complex physiology MeSH
- Humans MeSH
- Marriage * MeSH
- Reproduction genetics MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Accurate predictive modelling facilitates efficient and effective trait selection in animal breeding and can decrease costs while maximizing profits when raising economically important animals. The objective of this study was to extend a previously developed bioeconomic model and computer program to calculate the marginal economic values (MEVs) and economic weights (EWs) for direct and maternal pig traits affected by new reproductive traits, namely the number of sow functional teats (NFTs) and boar sperm quality traits (SQTs) that included sperm volume, sperm concentration, motility percentage and percentage of abnormal spermatozoa. The MEV of NFTs represented the cost differences between naturally and artificially reared piglets until weaning and the cost differences between naturally and artificially reared finished animals. The MEVs of SQTs expressed the saved costs for artificial insemination, assuming a decreased price per insemination dose when improving the SQTs. The absolute and relative EWs for the newly defined complex of traits in the breeding objectives for pig breeds involved in the Czech national three-way crossing system (Czech Large White [CLW], Czech Landrace [CL] and Pietrain [PN]) were calculated using gene flow methods. The NFT trait was included only for dam breeds, and the relative EW averaged 3.6% of the total economic importance based on the genetic standard deviations of all 19 simultaneously evaluated traits in CLW and CL breeds. The relative EWs of the four SQTs comprised 2.0% of the total economic importance of the 19 traits in the CLW and CL dam breeds and 8% of the total economic importance of the 18 traits in the PN sire breed. Therefore, inclusion of the NFTs for dam breeds and SQTs for sire breeds in the breeding goal is recommended to aid in obtaining ideal outcomes with optimal economic values.
- MeSH
- Animal Husbandry economics MeSH
- Breeding economics MeSH
- Models, Economic MeSH
- Phenotype * MeSH
- Mammary Glands, Animal * physiology MeSH
- Swine genetics physiology MeSH
- Reproduction genetics MeSH
- Selection, Genetic MeSH
- Spermatozoa * physiology MeSH
- Gene Flow MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
BACKGROUND: The castor bean tick Ixodes ricinus is an important vector of several clinically important diseases, whose prevalence increases with accelerating global climate changes. Characterization of a tick life-cycle is thus of great importance. However, researchers mainly focus on specific organs of fed life stages, while early development of this tick species is largely neglected. METHODS: In an attempt to better understand the life-cycle of this widespread arthropod parasite, we sequenced the transcriptomes of four life stages (egg, larva, nymph and adult female), including unfed and partially blood-fed individuals. To enable a more reliable identification of transcripts and their comparison in all five transcriptome libraries, we validated an improved-fit set of five I. ricinus-specific reference genes for internal standard normalization of our transcriptomes. Then, we mapped biological functions to transcripts identified in different life stages (clusters) to elucidate life stage-specific processes. Finally, we drew conclusions from the functional enrichment of these clusters specifically assigned to each transcriptome, also in the context of recently published transcriptomic studies in ticks. RESULTS: We found that reproduction-related transcripts are present in both fed nymphs and fed females, underlining the poorly documented importance of ovaries as moulting regulators in ticks. Additionally, we identified transposase transcripts in tick eggs suggesting elevated transposition during embryogenesis, co-activated with factors driving developmental regulation of gene expression. Our findings also highlight the importance of the regulation of energetic metabolism in tick eggs during embryonic development and glutamate metabolism in nymphs. CONCLUSIONS: Our study presents novel insights into stage-specific transcriptomes of I. ricinus and extends the current knowledge of this medically important pathogen, especially in the early phases of its development.
- MeSH
- Ixodes genetics growth & development MeSH
- Nymph growth & development MeSH
- Reproduction genetics MeSH
- Life Cycle Stages MeSH
- Gene Expression Profiling * MeSH
- Feeding Behavior MeSH
- Animals MeSH
- Check Tag
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
Recent studies of the distribution and diversity of freshwater zooplankton have indicated that the previously understudied Eastern Palearctic region is an important biogeographic hotspot. Here, we explored the lineage diversity and reproductive modes of the Daphnia pulex species group across China. Members of this group are often keystone species of standing water bodies and are frequently used as a model system for ecological, evolutionary and, more recently, genomic studies. We found members of the D. pulex group in seven of seventy-six Chinese water bodies examined. We analyzed their phylogenetic position using mitochondrial markers, and explored the genetic structure of six populations using microsatellite markers. Mitochondrial DNA analysis suggested the presence of two distinct species complexes in China: the D. pulex complex that has a global distribution, and an apparently endemic Eastern Palearctic D. mitsukuri complex. Microsatellite analyses of six populations suggested that three of these reproduced by cyclical parthenogenesis, as evidenced by high clonal diversity and the absence of deviations from the Hardy-Weinberg equilibrium. In contrast, three other populations showed remarkably low diversity of multilocus genotypes. This suggests an obligate parthenogenetic reproductive mode, which was confirmed in one of the populations by comparison of genotypes of Daphnia adults and dormant embryos. All presumably obligate parthenogenetic clones were heterozygous at the majority of microsatellite loci, suggesting their hybrid origin. This was further supported by analyses of a small GTPase nuclear gene (rab4), as two alleles within single individuals belonged to different clades. Interestingly, one putatively obligate parthenogenetic clone carried three distinct alleles suggesting higher ploidy and potential gene flow between the D. pulicaria and D. mitsukuri complexes. Our data show that the expansion of the D. pulex complex in the Eastern Palearctic was associated with widespread hybridization.
- MeSH
- Principal Component Analysis MeSH
- Daphnia classification genetics MeSH
- Phylogeny * MeSH
- Genetic Variation * MeSH
- Haplotypes MeSH
- Lakes * MeSH
- Microsatellite Repeats genetics MeSH
- DNA, Mitochondrial genetics MeSH
- Genes, Mitochondrial MeSH
- Likelihood Functions MeSH
- Reproduction genetics MeSH
- Geography MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- China MeSH
Chromozomové aberace jsou častou příčinou časných reprodukčních ztrát. Možnou přítomnost chromozomové aberace je možné ověřit cytogenetickým vyšetřením tkáně potraceného plodu. V rámci naší studie na Ústavu biologie a lékařské genetiky 1. lékařské fakulty Univerzity Karlovy a Všeobecné fakultní nemocnice v Praze jsme analyzovali vzorek tkáně u 233 případů časných spontánních či zamlklých potratů. Ve 212 případech byla kultivace úspěšná a celkem v 52 případech (24,5 %) byla zachycena chromozomová aberace – nejčastěji trizomie chromozomu 21, monozomie chromozomu X, triploidie a trizomie chromozomů 16 a 22. Celková četnost chromozomových aberací byla v našem souboru spíše nižší oproti obdobným studiím. I s ohledem na další ukazatele předpokládáme, že by příčinou mohla být kontaminace některých vzorků mateřskými buňkami, což ale nelze u rutinního cytogenetického vyšetření předem vyloučit. Dále jsme v rámci studie potvrdili vyšší četnost chromozomových aberací v případech s vyšším věkem matky a dále pak častější zastoupení chromozomových aberací v případech potratu ve vyšších týdnech těhotenství. Tyto nálezy byly statisticky významné.
Chromosomal aberrations are common cause of early miscarriage. Possible presence of chromosomal aberration may be assessed by cytogenetic examination of the aborted fetus tissue. In our study from the Institute of Biology and Medical Genetics of the First Faculty of Medicine of Charles University and General University Hospital in Prague we analysed tissue sample from 233 early spontaneous or missed abortions. In 212 cases the cultivation process was successful. Among those – we identified 52 cases with chromosomal aberration (24,5 %). Most common aberrations were – trisomy 21, monosomy X, triploidy and trisomies of chromosomes 16 and 22. Our overall incidence of aberrations was lower – compared to similar studies. According to other indicators we suppose that this may be caused by the higher incidence of maternal cells contamination – but this phenomenon cannot be completely excluded while using classical karyotyping. We also confirmed higher incidence of chromosomal aberrations in the miscarriage cases in elder mothers and furthermore we found higher incidence of aberrations in cases from higher gestation weeks. Both trends were statistically significant.
- Keywords
- reprodukční ztráty,
- MeSH
- Chromosome Aberrations * embryology classification statistics & numerical data MeSH
- Cytogenetic Analysis statistics & numerical data MeSH
- Genetic Fitness MeSH
- Karyotyping statistics & numerical data MeSH
- Humans MeSH
- Aborted Fetus abnormalities cytology MeSH
- Retrospective Studies MeSH
- Reproduction genetics MeSH
- Abortion, Spontaneous epidemiology etiology MeSH
- Pregnancy MeSH
- Age Factors MeSH
- Check Tag
- Humans MeSH
- Pregnancy MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czech Republic MeSH
Interspecific competition is a fundamental process affecting community structure and evolution of interacting species. Besides direct competition, this process is also mediated by shared enemies, which can change the outcome of competition dramatically. However, previous studies investigating interactions between competing species and their parasites (parasite-mediated competition) completely overlooked the effect of 'sperm' parasites (i.e. sperm-dependent parthenogens or pseudogams) on competition. These organisms originate by interspecific hybridization, produce clonal gametes, but exploit parental species for their own reproduction, being therefore analogous to classical parasites. Here we use the reaction-diffusion model and show that pseudogams alter the outcome of interspecific competition significantly. They may either slow down competitive exclusion of the inferior competitor or even turn the outcome of competition between the species. Asexual organisms may thus have unexpectedly strong impact on community structure, and have more significant evolutionary potential than was previously thought.
- MeSH
- Biological Evolution * MeSH
- Models, Biological MeSH
- Host-Parasite Interactions genetics MeSH
- Competitive Behavior physiology MeSH
- Reproduction genetics MeSH
- Sexual Behavior physiology MeSH
- Spermatozoa growth & development microbiology MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
